Variant report

Variant	rs9459654
Chromosome Location	chr6:166744444-166744445
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:134)
CpG islands
(count:61)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:134 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr6:166744057-166744520	K562	blood:	n/a	chr6:166744278-166744293 chr6:166744279-166744293 chr6:166744281-166744291 chr6:166744278-166744293
2	POLR2A	chr6:166743896-166744608	GM12878	blood:	n/a	n/a
3	NFIC	chr6:166744050-166744513	SK-N-SH	brain:	n/a	chr6:166744283-166744299 chr6:166744283-166744300
4	SP1	chr6:166744070-166744513	H1-hESC	embryonic stem cell:	n/a	chr6:166744303-166744313 chr6:166744298-166744308 chr6:166744271-166744292 chr6:166744297-166744308 chr6:166744450-166744464
5	MYC	chr6:166744045-166744537	K562	blood:	n/a	n/a
6	RAD21	chr6:166744068-166744522	H1-hESC	embryonic stem cell:	n/a	chr6:166744291-166744304
7	RAD21	chr6:166744096-166744466	SK-N-SH_RA	brain:	n/a	chr6:166744291-166744304
8	POLR2A	chr6:166743901-166744593	H1-hESC	embryonic stem cell:	n/a	n/a
9	HCFC1	chr6:166744087-166744539	K562	blood:	n/a	n/a
10	SMC3	chr6:166743979-166744580	HepG2	liver:	n/a	n/a
11	ARID3A	chr6:166744117-166744850	HepG2	liver:	n/a	n/a
12	CTCF	chr6:166744320-166744470	NHDF-neo	bronchial:	n/a	n/a
13	MXI1	chr6:166743827-166744730	SK-N-SH	brain:	n/a	n/a
14	TEAD4	chr6:166743945-166744638	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:166744030-166744549	GM12878	blood:	n/a	n/a
16	ZNF143	chr6:166744337-166744537	GM12878	blood:	n/a	n/a
17	NFIC	chr6:166743973-166744658	SK-N-SH	brain:	n/a	chr6:166744283-166744299 chr6:166744283-166744300
18	RCOR1	chr6:166744060-166744464	HepG2	liver:	n/a	n/a
19	RAD21	chr6:166744145-166744529	H1-hESC	embryonic stem cell:	n/a	chr6:166744291-166744304
20	CTCF	chr6:166744360-166744510	WI-38	lung:	n/a	n/a
21	NFIC	chr6:166743950-166744652	ECC-1	luminal epithelium:	n/a	chr6:166744283-166744299 chr6:166744283-166744300
22	CTCF	chr6:166744340-166744490	GM12871	blood:	n/a	n/a
23	POLR2A	chr6:166744346-166744461	GM12878	blood:	n/a	n/a
24	SP4	chr6:166744110-166744546	H1-hESC	embryonic stem cell:	n/a	chr6:166744297-166744308
25	TBL1XR1	chr6:166744122-166745211	K562	blood:	n/a	n/a
26	CTCF	chr6:166744300-166744450	RPTEC	kidney:	n/a	n/a
27	POLR2A	chr6:166744051-166744482	HepG2	liver:	n/a	n/a
28	CTCF	chr6:166743971-166744560	K562	blood:	n/a	chr6:166744232-166744245
29	USF1	chr6:166744139-166744465	K562	blood:	n/a	n/a
30	MAX	chr6:166744180-166744564	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:166744067-166744456	H1-hESC	embryonic stem cell:	n/a	n/a
32	RAD21	chr6:166744031-166744589	H1-hESC	embryonic stem cell:	n/a	chr6:166744291-166744304
33	POLR2A	chr6:166742700-166754624	K562	blood:	n/a	n/a
34	POLR2A	chr6:166743983-166744597	GM12892	blood:	n/a	n/a
35	TAF1	chr6:166744043-166744541	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:166744040-166744527	GM12891	blood:	n/a	n/a
37	HDAC2	chr6:166744082-166744462	H1-hESC	embryonic stem cell:	n/a	n/a
38	UBTF	chr6:166744066-166744521	K562	blood:	n/a	n/a
39	CTCF	chr6:166744300-166744450	AoAF	blood vessel:	n/a	n/a
40	ARID3A	chr6:166743832-166744548	K562	blood:	n/a	n/a
41	CTCF	chr6:166744183-166744508	GM12878	blood:	n/a	chr6:166744232-166744245
42	CTCF	chr6:166744124-166744528	HepG2	liver:	n/a	chr6:166744232-166744245
43	CTCF	chr6:166744223-166744458	MCF-7	breast:	n/a	chr6:166744232-166744245
44	CTCF	chr6:166744128-166744483	K562	blood:	n/a	chr6:166744232-166744245
45	MAX	chr6:166744056-166744560	K562	blood:	n/a	n/a
46	POLR2A	chr6:166744101-166744467	H1-hESC	embryonic stem cell:	n/a	n/a
47	UBTF	chr6:166744149-166744630	K562	blood:	n/a	n/a
48	POU2F2	chr6:166744052-166744524	GM12878	blood:	n/a	n/a
49	EP300	chr6:166744114-166744482	H1-hESC	embryonic stem cell:	n/a	n/a
50	CTCF	chr6:166744340-166744490	HCM	heart:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:166744404-166744454	AG09309	skin:	n/a
2	chr6:166744404-166744454	MCF-7	breast:	n/a
3	chr6:166744404-166744454	Jurkat	blood:	n/a
4	chr6:166744404-166744454	NHBE	bronchial:	n/a
5	chr6:166744404-166744454	AG09319	gingival:	n/a
6	chr6:166744404-166744454	HL-60	blood:	n/a
7	chr6:166744404-166744454	HMEC	breast:	n/a
8	chr6:166744404-166744454	HCPEpiC	choroid plexus:	n/a
9	chr6:166744404-166744454	MCF10A-Er-Src	breast:	n/a
10	chr6:166744404-166744454	SKMC	muscle:	n/a
11	chr6:166744404-166744454	BE2_C	brain:	n/a
12	chr6:166744404-166744454	CMK	blood:	n/a
13	chr6:166744404-166744454	GM12878	blood:	n/a
14	chr6:166744404-166744454	K562	blood:	n/a
15	chr6:166744404-166744454	HRPEpiC	eye:	n/a
16	chr6:166744404-166744454	ovcar-3	ovarian:	n/a
17	chr6:166744404-166744454	Hela-S3	cervix:	n/a
18	chr6:166744404-166744454	IMR90	lung:	fetal
19	chr6:166744404-166744454	HRCEpiC	kidney:	n/a
20	chr6:166744404-166744454	HEK293	kidney:	embryo
21	chr6:166744404-166744454	HIPEpiC	eye:	n/a
22	chr6:166744404-166744454	HRE	kidney:	n/a
23	chr6:166744404-166744454	AoSMC	blood vessel:	n/a
24	chr6:166744404-166744454	HPAEpiC	pulmonary alveolar:	n/a
25	chr6:166744404-166744454	AG04450	lung:	fetal
26	chr6:166744404-166744454	PFSK-1	brain:	n/a
27	chr6:166744404-166744454	SK-N-MC	brain:	n/a
28	chr6:166744404-166744454	GM06990	blood:	n/a
29	chr6:166744404-166744454	SK-N-SH_RA	brain:	n/a
30	chr6:166744404-166744454	HCT-116	colon:	n/a
31	chr6:166744404-166744454	Caco-2	colon:	n/a
32	chr6:166744404-166744454	HUVEC	blood vessel:	n/a
33	chr6:166744404-166744454	SK-N-SH	brain:	n/a
34	chr6:166744404-166744454	AG04449	skin:	fetal
35	chr6:166744404-166744454	GM12891	blood:	n/a
36	chr6:166744404-166744454	ProgFib	skin:	n/a
37	chr6:166744404-166744454	SAEC	small airway:	n/a
38	chr6:166744404-166744454	BJ	skin:	n/a
39	chr6:166744404-166744454	HepG2	liver:	n/a
40	chr6:166744404-166744454	NHDF-neo	bronchial:	n/a
41	chr6:166744404-166744454	Hepatocyte	liver:	n/a
42	chr6:166744404-166744454	PANC-1	pancreas:	n/a
43	chr6:166744404-166744454	HCM	heart:	n/a
44	chr6:166744404-166744454	AG10803	skin:	n/a
45	chr6:166744404-166744454	H1-hESC	embryonic stem cell:	embryo
46	chr6:166744404-166744454	HNPCEpiC	eye:	n/a
47	chr6:166744404-166744454	GM19239	blood:	n/a
48	chr6:166744404-166744454	LNCaP	prostate:	n/a
49	chr6:166744404-166744454	HEEpiC	esophagus:	n/a
50	chr6:166744404-166744454	PrEC	prostate:	n/a

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:166743880..166744818-chr6:166814023..166814944,3	K562	blood:
2	chr6:166738156..166741727-chr6:166741924..166746289,6	K562	blood:
3	chr6:166689019..166690684-chr6:166742246..166744543,2	K562	blood:
4	chr6:166743853..166744743-chr6:166794927..166795865,3	K562	blood:
5	chr6:166743072..166748840-chr6:166793771..166798653,8	K562	blood:
6	chr6:166744077..166744772-chr6:166795075..166795860,2	MCF-7	breast:

No data

Variant related genes	Relation type
HNRNPA1P49	TF binding region
SFT2D1	TF binding region
HNRNPA1P49	CpG island
SFT2D1	CpG island
ENSG00000060762	Chromatin interaction
ENSG00000198818	Chromatin interaction
ENSG00000261420	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10806847	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10862	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11168	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2343590	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4470829	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4598048	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4709112	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4710041	0.82[AMR][1000 genomes]
rs6909951	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6918901	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6927168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7757549	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9355572	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9356476	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9356479	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9366005	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9366006	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9366007	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886934	chr6:166642850-166747572	Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv3490076	chr6:166727901-167306743	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
3	esv3490077	chr6:166727901-167306743	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9459654	SFT2D1	cis	Whole Blood	GTEx
rs9459654	HNRNPA1P49	cis	lung	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:166729000-166745400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:166732400-166744600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr6:166732400-166751600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr6:166733200-166753600	Weak transcription	Fetal Heart	heart
5	chr6:166733800-166749600	Weak transcription	Psoas Muscle	Psoas
6	chr6:166733800-166753800	Weak transcription	Hela-S3	cervix
7	chr6:166734600-166754800	Weak transcription	HUVEC	blood vessel
8	chr6:166737000-166745600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr6:166738200-166754200	Weak transcription	NH-A	brain
10	chr6:166739400-166745400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:166739400-166746800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:166739400-166748000	Weak transcription	Gastric	stomach
13	chr6:166739400-166755400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:166740000-166750800	Weak transcription	HSMMtube	muscle
15	chr6:166740400-166748600	Weak transcription	Brain Germinal Matrix	brain
16	chr6:166741400-166746600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr6:166741400-166750000	Weak transcription	HMEC	breast
18	chr6:166741400-166752400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:166741600-166746400	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:166742200-166744600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:166742200-166746600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr6:166742200-166751200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr6:166742400-166744800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr6:166742400-166748200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:166742600-166745600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:166742600-166746200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:166742600-166746400	Weak transcription	Placenta	Placenta
28	chr6:166742600-166746400	Weak transcription	Lung	lung
29	chr6:166742600-166754000	Weak transcription	Fetal Kidney	kidney
30	chr6:166742800-166745200	Weak transcription	Primary T helper cells PMA-I stimulated	--
31	chr6:166742800-166745400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr6:166742800-166745800	Weak transcription	Spleen	Spleen
33	chr6:166742800-166746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:166742800-166746200	Weak transcription	Fetal Intestine Small	intestine
35	chr6:166742800-166746200	Weak transcription	Osteobl	bone
36	chr6:166742800-166746400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr6:166742800-166746400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr6:166742800-166746400	Weak transcription	Aorta	Aorta
39	chr6:166742800-166746400	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:166742800-166746600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:166742800-166746800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr6:166742800-166747000	Weak transcription	Rectal Smooth Muscle	rectum
43	chr6:166742800-166748400	Weak transcription	Rectal Mucosa Donor 29	rectum
44	chr6:166742800-166749200	Weak transcription	NHEK	skin
45	chr6:166742800-166750000	Weak transcription	Colonic Mucosa	Colon
46	chr6:166742800-166751000	Weak transcription	HSMM	muscle
47	chr6:166743000-166745200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr6:166743000-166745400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr6:166743000-166745800	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:166743000-166746200	Weak transcription	Primary B cells from cord blood	blood

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